Best practices for the extraction of genomic DNA from formalin‐fixed paraffin‐embedded tumor tissue for cancer genomic profiling tests

Recently, two cancer genomic profiling tests have been approved in Japan and implemented in routine clinical practice: the FDA‐approved FoundationOne CDx test, and the OncoGuide NCC Oncopanel test. The quality and quantity of DNA significantly affects the sequencing results; therefore, preparing a sufficient amount of high‐quality DNA for clinical cancer genomic profiling tests is important. We examined the best practices for the extraction of cancer genomic DNA from formalin‐fixed paraffin‐embedded (FFPE) tumor tissues of pancreatic, lung and colon cancer specimens. We found that the quality of cancer genomic DNA extracted from 10‐μm‐thick FFPE samples improved significantly, compared with that from 4‐μm‐thick FFPE samples, suggesting that 10‐μm‐thick FFPE samples are preferable for clinical cancer genomic profiling tests. For convenience, we created a quick reference table for calculating the required number of FFPE slides.

This is the peer reviewed version of the following article: Hirofumi Inoue et. al. Best practices for the extraction of genomic DNA from formalin‐fixed paraffin‐embedded tumor tissue for cancer genomic profiling tests. Pathology International (2021), which has been published in final form at https://doi.org/10.1111/pin.13086. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions.
This fulltext is available in March 2022.